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- PDB-3hjv: 1.7 Angstrom resolution crystal structure of an acyl carrier prot... -

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Basic information

Entry
Database: PDB / ID: 3hjv
Title1.7 Angstrom resolution crystal structure of an acyl carrier protein S-malonyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsMalonyl Coa-acyl carrier protein transacylase
KeywordsTRANSFERASE / Acyl Carrier Protein S-malonyltransferase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
butyl acetate / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Anderson, S. / Skarina, T. / Onopriyenko, O. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.7 Angstrom resolution crystal structure of an acyl carrier protein S-malonyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Halavaty, A.S. / Wawrzak, Z. / Anderson, S. / Skarina, T. / Onopriyenko, O. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl Coa-acyl carrier protein transacylase
B: Malonyl Coa-acyl carrier protein transacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73536
Polymers67,2432
Non-polymers3,49234
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-349 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.525, 87.789, 121.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malonyl Coa-acyl carrier protein transacylase


Mass: 33621.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: Vibrio cholerae O1 biovar eltor str. N16961 / Gene: VC_2022 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q9KQH6

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Non-polymers , 5 types, 697 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-8JZ / butyl acetate / Butyl acetate


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 11
Details: The home made "Pioneer" screen, condition 11, mixed at 1:1 v/v ratio with protein sample (16 mg/mL, 0.3 M NaCl and 0.5 mM TCEP, 10mM Hepes pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 105566 / Num. obs: 105566 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 26.27
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.48 / Num. unique all: 9855 / % possible all: 92.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
REFMAC5.5.0051refinement
HKL-2000data reduction
XDSdata reduction
HKL-2000data scaling
XSCALEdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
Bp3phasing
SOLOMONphasing
ARP/wARPin CCP4model building
RefinementMethod to determine structure: SAD / Resolution: 1.7→43.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.506 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19314 2841 5.1 %RANDOM
Rwork0.14521 ---
all0.14764 52586 --
obs0.14764 52586 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.998 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 191 663 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225315
X-RAY DIFFRACTIONr_bond_other_d0.0010.023489
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.0147301
X-RAY DIFFRACTIONr_angle_other_deg0.93338706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6055715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10826.548197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59115893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8061516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216023
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02909
X-RAY DIFFRACTIONr_mcbond_it0.681.53375
X-RAY DIFFRACTIONr_mcbond_other0.1991.51349
X-RAY DIFFRACTIONr_mcangle_it1.2425488
X-RAY DIFFRACTIONr_scbond_it2.25731940
X-RAY DIFFRACTIONr_scangle_it3.6944.51812
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 184 -
Rwork0.224 3687 -
obs-3687 94.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2374-0.3944-0.87162.98240.40430.7835-0.02550.10970.1154-0.05490.0733-0.066-0.04880.0171-0.04780.0091-0.0091-0.00040.02420.01040.010557.522100.62892.8698
20.7565-0.00380.04440.54790.03210.3934-0.0171-0.0136-0.00760.00830.02270.00780.0228-0.0346-0.00560.01940.00330.00640.0170.00780.004942.076981.49487.8366
32.6641-0.1355-1.10853.88420.83091.744-0.0257-0.09540.1037-0.11880.11910.017-0.1455-0.0772-0.09340.03340.01150.00220.0314-0.00910.032335.9536101.6589-17.9833
41.3507-0.0073-0.1260.5552-0.32150.95070.0051-0.0445-0.1025-0.02340.00520.01980.05590.0367-0.01020.0175-0.00180.00090.00530.00180.009450.730581.9879-23.9858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A130 - 205
2X-RAY DIFFRACTION2A6 - 129
3X-RAY DIFFRACTION2A206 - 312
4X-RAY DIFFRACTION3B130 - 205
5X-RAY DIFFRACTION4B7 - 129
6X-RAY DIFFRACTION4B206 - 312

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